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Deciphering the ovarian cancer ascites fluid peptidome.

Bery A, Leung F, Smith CR, Diamandis EP, Kulasingam V - Clin Proteomics (2014)

Bottom Line: The resultant fractions were analyzed using an Orbitrap mass spectrometer.We identified over 2000 unique endogenous peptides derived from 259 proteins.Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. vathany.kulasingam@uhn.ca.

ABSTRACT

Background: Conventional proteomic approaches have thus far been unable to identify novel serum biomarkers for ovarian cancer that are more sensitive and specific than the current clinically used marker, CA-125. Because endogenous peptides are smaller and may enter the circulation more easily than proteins, a focus on the low-molecular-weight region may reveal novel biomarkers with enhanced sensitivity and specificity. In this study, we deciphered the peptidome of ascites fluid from 3 ovarian cancer patients and 3 benign individuals (ascites fluid from patients with liver cirrhosis).

Results: Following ultrafiltration of the ascites fluids to remove larger proteins, each filtrate was subjected to solid phase extraction and fractionated using strong cation exchange chromatography. The resultant fractions were analyzed using an Orbitrap mass spectrometer. We identified over 2000 unique endogenous peptides derived from 259 proteins. We then catalogued over 777 peptides that were found only in ovarian cancer ascites. Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

Conclusions: Peptidomics may uncover previously undiscovered disease-specific endogenous peptides that warrant further investigation as biomarkers for ovarian cancer.

No MeSH data available.


Related in: MedlinePlus

Outline of experimental workflow (peptidomic analysis). The workflow consisted of the following: sample processing, followed by strong cation exchange and reverse-phase chromatography coupled online to an LTQ-Orbitrap mass spectrometer and subsequent data analysis.
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Figure 1: Outline of experimental workflow (peptidomic analysis). The workflow consisted of the following: sample processing, followed by strong cation exchange and reverse-phase chromatography coupled online to an LTQ-Orbitrap mass spectrometer and subsequent data analysis.

Mentions: Using the experimental workflow depicted in Figure 1, we elucidated the endogenous peptidome of 6 ascites fluid samples, 3 from OvCa patients and 3 from non-cancer controls. This is, to our knowledge, the first study to mine the low-molecular-weight region of OvCa ascites. We identified 2066 unique peptides (Additional file 1), 777 of which were found in OvCa but not in the control samples. The 777 OvCa-specific peptides corresponded to only 59 proteins, indicating that many of the peptides identified are degradation products of the same parent proteins. The list of the 59 parent proteins and the corresponding 777 unique peptides is provided in Additional file 2A and B. A full spectrum report, which includes information about modifications associated with each peptide, is provided in Additional file 3. Figure 2 (A) and (B) display the overlap of identified proteins and peptides between the benign and OvCa samples, respectively. Interestingly, our study identified a larger number of peptides from benign samples than from OvCa samples, suggesting that protease activity alone may not be sufficient to discriminate cancerous from benign ascites fluid. Our benign ascites fluid originated from patients with cirrhosis of the liver, a condition associated with a rise in both inflammatory mediators and matrix metalloproteases [14-17].


Deciphering the ovarian cancer ascites fluid peptidome.

Bery A, Leung F, Smith CR, Diamandis EP, Kulasingam V - Clin Proteomics (2014)

Outline of experimental workflow (peptidomic analysis). The workflow consisted of the following: sample processing, followed by strong cation exchange and reverse-phase chromatography coupled online to an LTQ-Orbitrap mass spectrometer and subsequent data analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230032&req=5

Figure 1: Outline of experimental workflow (peptidomic analysis). The workflow consisted of the following: sample processing, followed by strong cation exchange and reverse-phase chromatography coupled online to an LTQ-Orbitrap mass spectrometer and subsequent data analysis.
Mentions: Using the experimental workflow depicted in Figure 1, we elucidated the endogenous peptidome of 6 ascites fluid samples, 3 from OvCa patients and 3 from non-cancer controls. This is, to our knowledge, the first study to mine the low-molecular-weight region of OvCa ascites. We identified 2066 unique peptides (Additional file 1), 777 of which were found in OvCa but not in the control samples. The 777 OvCa-specific peptides corresponded to only 59 proteins, indicating that many of the peptides identified are degradation products of the same parent proteins. The list of the 59 parent proteins and the corresponding 777 unique peptides is provided in Additional file 2A and B. A full spectrum report, which includes information about modifications associated with each peptide, is provided in Additional file 3. Figure 2 (A) and (B) display the overlap of identified proteins and peptides between the benign and OvCa samples, respectively. Interestingly, our study identified a larger number of peptides from benign samples than from OvCa samples, suggesting that protease activity alone may not be sufficient to discriminate cancerous from benign ascites fluid. Our benign ascites fluid originated from patients with cirrhosis of the liver, a condition associated with a rise in both inflammatory mediators and matrix metalloproteases [14-17].

Bottom Line: The resultant fractions were analyzed using an Orbitrap mass spectrometer.We identified over 2000 unique endogenous peptides derived from 259 proteins.Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. vathany.kulasingam@uhn.ca.

ABSTRACT

Background: Conventional proteomic approaches have thus far been unable to identify novel serum biomarkers for ovarian cancer that are more sensitive and specific than the current clinically used marker, CA-125. Because endogenous peptides are smaller and may enter the circulation more easily than proteins, a focus on the low-molecular-weight region may reveal novel biomarkers with enhanced sensitivity and specificity. In this study, we deciphered the peptidome of ascites fluid from 3 ovarian cancer patients and 3 benign individuals (ascites fluid from patients with liver cirrhosis).

Results: Following ultrafiltration of the ascites fluids to remove larger proteins, each filtrate was subjected to solid phase extraction and fractionated using strong cation exchange chromatography. The resultant fractions were analyzed using an Orbitrap mass spectrometer. We identified over 2000 unique endogenous peptides derived from 259 proteins. We then catalogued over 777 peptides that were found only in ovarian cancer ascites. Our list of peptides found in ovarian cancer specimens includes fragments derived from the proteins vitronectin, transketolase and haptoglobin.

Conclusions: Peptidomics may uncover previously undiscovered disease-specific endogenous peptides that warrant further investigation as biomarkers for ovarian cancer.

No MeSH data available.


Related in: MedlinePlus